Genetic Variant GPR85:p.Gly84Gly (chr7-113084470-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001146267.2(GPR85):c.252T>C(p.Gly84Gly) variant causes a synonymous change. The variant allele was found at a frequency of 0.885 in 1,613,626 control chromosomes in the GnomAD database, including 633,212 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.89 ( 60113 hom., cov: 31)

Exomes 𝑓: 0.89 ( 573099 hom. )

Consequence

GPR85
NM_001146267.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.73

Publications

17 publications found

Variant links:

Genes affected

GPR85 (HGNC:4536): (G protein-coupled receptor 85) Members of the G protein-coupled receptor (GPCR) family, such as GPR85, have a similar structure characterized by 7 transmembrane domains. Activation of GPCRs by extracellular stimuli, such as neurotransmitters, hormones, or light, induces an intracellular signaling cascade mediated by heterotrimeric GTP-binding proteins, or G proteins (Matsumoto et al., 2000 [PubMed 10833454]).[supplied by OMIM, Aug 2008]

GPR85 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR85	NM_001146267.2 link	c.252T>C	p.Gly84Gly	synonymous_variant	Exon 3 of 3	ENST00000424100.2	NP_001139739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000424100.2 link	c.252T>C	p.Gly84Gly	synonymous_variant	Exon 3 of 3	1	NM_001146267.2	ENSP00000396763.1

Frequencies

GnomAD3 genomes

AF:

0.888

AC:

135062

AN:

152042

Hom.:

60060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.888

Gnomad AMI

AF:

0.760

Gnomad AMR

AF:

0.917

Gnomad ASJ

AF:

0.867

Gnomad EAS

AF:

0.976

Gnomad SAS

AF:

0.818

Gnomad FIN

AF:

0.891

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.892

GnomAD2 exomes

AF:

0.891

AC:

224105

AN:

251414

AF XY:

0.885

show subpopulations

Gnomad AFR exome

AF:

0.887

Gnomad AMR exome

AF:

0.948

Gnomad ASJ exome

AF:

0.867

Gnomad EAS exome

AF:

0.977

Gnomad FIN exome

AF:

0.891

Gnomad NFE exome

AF:

0.883

Gnomad OTH exome

AF:

0.889

GnomAD4 exome

AF:

0.885

AC:

1293587

AN:

1461466

Hom.:

573099

Cov.:

AF XY:

0.883

AC XY:

641698

AN XY:

727084

show subpopulations

African (AFR)

AF:

0.885

AC:

29639

AN:

33474

American (AMR)

AF:

0.945

AC:

42253

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.869

AC:

22700

AN:

26134

East Asian (EAS)

AF:

0.980

AC:

38914

AN:

39700

South Asian (SAS)

AF:

0.823

AC:

71013

AN:

86250

European-Finnish (FIN)

AF:

0.891

AC:

47592

AN:

53416

Middle Eastern (MID)

AF:

0.834

AC:

4808

AN:

5768

European-Non Finnish (NFE)

AF:

0.884

AC:

983135

AN:

1111626

Other (OTH)

AF:

0.887

AC:

53533

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

8672

17345

26017

34690

43362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21374

42748

64122

85496

106870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.888

AC:

135175

AN:

152160

Hom.:

60113

Cov.:

AF XY:

0.887

AC XY:

65994

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.887

AC:

36834

AN:

41506

American (AMR)

AF:

0.917

AC:

14016

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.867

AC:

3010

AN:

3472

East Asian (EAS)

AF:

0.976

AC:

5035

AN:

5160

South Asian (SAS)

AF:

0.818

AC:

3943

AN:

4818

European-Finnish (FIN)

AF:

0.891

AC:

9437

AN:

10596

Middle Eastern (MID)

AF:

0.789

AC:

232

AN:

294

European-Non Finnish (NFE)

AF:

0.884

AC:

60085

AN:

67998

Other (OTH)

AF:

0.894

AC:

1890

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

764

1528

2293

3057

3821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

902

1804

2706

3608

4510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.885

Hom.:

48025

Bravo

AF:

0.892

Asia WGS

AF:

0.913

AC:

3172

AN:

3478

EpiCase

AF:

0.878

EpiControl

AF:

0.879

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

9.3

(source)

DANN

Benign

0.66

PhyloP100

4.7

Mutation Taster

=96/4

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over